Part of the SMCRA data structure, UnityMolStructure stores the models of the structure More...

Public Types
enum	MolecularType { MolecularType.standard, MolecularType.Martini, MolecularType.OPEP, MolecularType.HIRERNA }

Public Member Functions
	UnityMolStructure (List< UnityMolModel > listModels, string nameStructure)
	UnityMolStructure constructor taking a list of models as arg More...

	UnityMolStructure (UnityMolModel newModel, string nameStructure)
	UnityMolStructure constructor taking a model as arg More...

void	updateAtomRepValues ()
	Update atom radii and colors of all atoms based on the detected structure molecular type (Martini/HireRNA...) More...

void	readTrajectoryXDR (string trajPath)

void	unloadTrajectoryXDR ()

void	readDX (string dxPath)

void	unloadDX ()

void	createModelPlayer ()

void	modelNext (bool forward=true, bool loop=true)

void	setModel (int modelId)

void	trajNext (bool forward=true, bool loop=true)

void	trajNextSmooth (float t, bool forward=true, bool loop=true, bool newFrame=false)

void	trajSetFrame (int idF)

void	updateRepresentations (bool trajectory=true)
	Update positions of GameObject recorded in atomToGo and update representations with new positions More...

void	trajUpdateAtomPositions ()
	Updates each atom position of the current model of the structure based on the trajectory Uses center of gravity from the first model of the structure ! More...

void	createTrajectoryPlayer ()

List< UnityMolStructure >	splitModelsInStructures ()
	Split different models read in a file into several UnityMolStructure More...

UnityMolAtom	findAtomInModel (UnityMolModel newModel, UnityMolAtom prevAtom, bool strict=false)
	Find the corresponding atom from a model to a different model Returns null if not found More...

UnityMolSelection	ToSelectionAll ()
	Outputs a UnityMolSelection of all the atoms of the structure, including the atoms of the different models More...

UnityMolSelection	ToSelection ()
	Outputs a UnityMolSelection of all the atoms of the current model of structure More...

string	ToSelectionName ()

string	formatName (int length)

void	AddAtom (UnityMolAtom toAdd, string modelName, string chainName)

Vector3 []	getColliderPositions ()

GameObject []	getAtomGos ()

void	disconnectIMD ()

Public Attributes
List< UnityMolModel >	models
	Store all the models of the structure More...

string	name
	Parsed structure name More...

string	uniqueName
	Unique structure name More...

MolecularType	structureType = MolecularType.standard
	Identified type of molecular structure (all-atoms/Martini/Hire-RNA/OPEP) More...

List< UnityMolRepresentation >	representations
	List of representations for this structure More...

bool	trajectoryLoaded = false
	Trajectory loaded for this structure More...

List< Vector3 >	trajAtomPositions
	Atom positions used when reading a trajectory file More...

XDRFileReader	xdr
	Trajectory reader using xdrfile library More...

ArtemisManager	artemisM
	Trajectory reader using xdrfile library More...

TrajectoryPlayer	trajPlayer
	Trajectory player calling trajNext from a monobehaviour Update loop More...

DXReader	dxr
	Dx file reader More...

bool	ssInfoFromFile = false
	Secondary structures were parsed More...

int	currentModelId = 0
	Current model id used More...

ModelsPlayer	modelsPlayer
	Monobehaviour script to read models like trajectories More...

int	groupID = 0
	Id of the group used to move the molecules More...

Dictionary< UnityMolAtom, GameObject >	atomToGo
	Associates a GameObject with an UnityMolAtom More...

Properties
UnityMolModel	currentModel `[get]`
	Current model used More...

int	Count `[get]`
	Returns the number of atoms in the current model More...

int	Length `[get]`
	Returns the number of atoms in the current model More...

Detailed Description

Part of the SMCRA data structure, UnityMolStructure stores the models of the structure

Member Enumeration Documentation

◆ MolecularType

enum UMol.UnityMolStructure.MolecularType

strong

Enumerator
standard
Martini
OPEP
HIRERNA

Constructor & Destructor Documentation

◆ UnityMolStructure() [1/2]

UMol.UnityMolStructure.UnityMolStructure	(	List< UnityMolModel >	listModels,
		string	nameStructure
	)

UnityMolStructure constructor taking a list of models as arg

◆ UnityMolStructure() [2/2]

UMol.UnityMolStructure.UnityMolStructure	(	UnityMolModel	newModel,
		string	nameStructure
	)

UnityMolStructure constructor taking a model as arg

Member Function Documentation

◆ AddAtom()

void UMol.UnityMolStructure.AddAtom	(	UnityMolAtom	toAdd,
		string	modelName,
		string	chainName
	)

◆ createModelPlayer()

void UMol.UnityMolStructure.createModelPlayer ( )

◆ createTrajectoryPlayer()

void UMol.UnityMolStructure.createTrajectoryPlayer ( )

◆ disconnectIMD()

void UMol.UnityMolStructure.disconnectIMD ( )

◆ findAtomInModel()

UnityMolAtom UMol.UnityMolStructure.findAtomInModel	(	UnityMolModel	newModel,
		UnityMolAtom	prevAtom,
		bool	strict = `false`
	)

Find the corresponding atom from a model to a different model Returns null if not found

◆ formatName()

string UMol.UnityMolStructure.formatName ( int length )

◆ getAtomGos()

GameObject [] UMol.UnityMolStructure.getAtomGos ( )

◆ getColliderPositions()

Vector3 [] UMol.UnityMolStructure.getColliderPositions ( )

◆ modelNext()

void UMol.UnityMolStructure.modelNext	(	bool	forward = `true`,
		bool	loop = `true`
	)

◆ readDX()

void UMol.UnityMolStructure.readDX ( string dxPath )

◆ readTrajectoryXDR()

void UMol.UnityMolStructure.readTrajectoryXDR ( string trajPath )

◆ setModel()

void UMol.UnityMolStructure.setModel ( int modelId )

◆ splitModelsInStructures()

List<UnityMolStructure> UMol.UnityMolStructure.splitModelsInStructures ( )

Split different models read in a file into several UnityMolStructure

◆ ToSelection()

UnityMolSelection UMol.UnityMolStructure.ToSelection ( )

Outputs a UnityMolSelection of all the atoms of the current model of structure

◆ ToSelectionAll()

UnityMolSelection UMol.UnityMolStructure.ToSelectionAll ( )

Outputs a UnityMolSelection of all the atoms of the structure, including the atoms of the different models

◆ ToSelectionName()

string UMol.UnityMolStructure.ToSelectionName ( )

◆ trajNext()

void UMol.UnityMolStructure.trajNext	(	bool	forward = `true`,
		bool	loop = `true`
	)

◆ trajNextSmooth()

void UMol.UnityMolStructure.trajNextSmooth	(	float	t,
		bool	forward = `true`,
		bool	loop = `true`,
		bool	newFrame = `false`
	)

◆ trajSetFrame()

void UMol.UnityMolStructure.trajSetFrame ( int idF )

◆ trajUpdateAtomPositions()

void UMol.UnityMolStructure.trajUpdateAtomPositions ( )

Updates each atom position of the current model of the structure based on the trajectory Uses center of gravity from the first model of the structure !

◆ unloadDX()

void UMol.UnityMolStructure.unloadDX ( )

◆ unloadTrajectoryXDR()

void UMol.UnityMolStructure.unloadTrajectoryXDR ( )

◆ updateAtomRepValues()

void UMol.UnityMolStructure.updateAtomRepValues ( )

Update atom radii and colors of all atoms based on the detected structure molecular type (Martini/HireRNA...)

◆ updateRepresentations()

void UMol.UnityMolStructure.updateRepresentations ( bool trajectory = true )

Update positions of GameObject recorded in atomToGo and update representations with new positions

Member Data Documentation

◆ artemisM

ArtemisManager UMol.UnityMolStructure.artemisM

Trajectory reader using xdrfile library

◆ atomToGo

Dictionary<UnityMolAtom, GameObject> UMol.UnityMolStructure.atomToGo

Associates a GameObject with an UnityMolAtom

◆ currentModelId

int UMol.UnityMolStructure.currentModelId = 0

Current model id used

◆ dxr

DXReader UMol.UnityMolStructure.dxr

Dx file reader

◆ groupID

int UMol.UnityMolStructure.groupID = 0

Id of the group used to move the molecules

◆ models

List<UnityMolModel> UMol.UnityMolStructure.models

Store all the models of the structure

◆ modelsPlayer

ModelsPlayer UMol.UnityMolStructure.modelsPlayer

Monobehaviour script to read models like trajectories

◆ name

string UMol.UnityMolStructure.name

Parsed structure name

◆ representations

List<UnityMolRepresentation> UMol.UnityMolStructure.representations

List of representations for this structure

◆ ssInfoFromFile

bool UMol.UnityMolStructure.ssInfoFromFile = false

Secondary structures were parsed

◆ structureType

MolecularType UMol.UnityMolStructure.structureType = MolecularType.standard

Identified type of molecular structure (all-atoms/Martini/Hire-RNA/OPEP)

◆ trajAtomPositions

List<Vector3> UMol.UnityMolStructure.trajAtomPositions

Atom positions used when reading a trajectory file

◆ trajectoryLoaded

bool UMol.UnityMolStructure.trajectoryLoaded = false

Trajectory loaded for this structure

◆ trajPlayer

TrajectoryPlayer UMol.UnityMolStructure.trajPlayer

Trajectory player calling trajNext from a monobehaviour Update loop

◆ uniqueName

string UMol.UnityMolStructure.uniqueName

Unique structure name

◆ xdr

XDRFileReader UMol.UnityMolStructure.xdr